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e76b79a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | # Protein programming language
This repository contains an implementation of the programming language described in the paper [A high-level programming language for generative protein design](https://www.biorxiv.org/content/10.1101/2022.12.21.521526v1).
## Tutorial
We have provided a [tutorial notebook](tutorial.ipynb) describing the basics of writing programs and running optimization loops.
The notebook can be run in Colab:
[<img src="https://colab.research.google.com/assets/colab-badge.svg">](https://colab.research.google.com/github/facebookresearch/esm/blob/main/examples/protein-programming-language/tutorial.ipynb)
## Design programs
We have also provided some example programs as described in our original paper.
| Design task | Figure in paper | Program file |
|:--------------------------------------------|:----------------|:----------------------------------------------------------------------------|
| Free hallucination | Figure 2A | [free_hallucination.py](programs/free_hallucination.py) |
| Fixed backbone design | Figure 2D | [fixed_backbone.py](programs/fixed_backbone.py) |
| Secondary structure design | Figure 2G | [secondary_structure.py](programs/secondary_structure.py) |
| Functional site scaffolding | Figure 2H | [functional_site_scaffolding.py](programs/functional_site_scaffolding.py) |
| Symmetric monomer design | Figure 3A | [symmetric_monomer.py](programs/symmetric_monomer.py) |
| Two-level symmetric<br>homo-oligomer design | Figure 4A | [symmetric_two_level_multimer.py](programs/symmetric_two_level_multimer.py) |
| Symmetric binding site<br>scaffolding | Figure 5A | [symmetric_binding.py](programs/symmetric_binding.py) |
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